getReadonly {GeneOverlap} | R Documentation |
The intersection and union slots contain the gene names as character vectors. The is.tested slot contains a Boolean label indicating whether the object has been tested or not. The cont.tbl slot contains the contingency table as a matrix. The pval and odds.ratio slots contain the p-value and odds ratio as numerics, respectively. The Jaccard slot contains the Jaccard index as a numeric.
## S4 method for signature 'GeneOverlap' getIntersection(object) ## S4 method for signature 'GeneOverlap' getUnion(object) ## S4 method for signature 'GeneOverlap' getTested(object) ## S4 method for signature 'GeneOverlap' getContbl(object) ## S4 method for signature 'GeneOverlap' getPval(object) ## S4 method for signature 'GeneOverlap' getOddsRatio(object) ## S4 method for signature 'GeneOverlap' getJaccard(object)
object |
A GeneOverlap object. |
If the GeneOverlap object has not been tested yet, the returned Jaccard index, p-value and odds ratio will be NA, the contingency table will be an empty matrix.
intersection |
A character vector represents the overlapped genes. |
union |
A character vector represents the genes in the union of A and B. |
is.tested |
A Boolean represents whether the overlapping test has been performed or not. |
cont.tbl |
A matrix represents the contingency table. |
pval |
A numeric represents the significance of overlap. |
odds.ratio |
A numeric represents the odds ratio in comparison to the genomic background. |
Jaccard |
A numeric represents the Jaccard index between two sets. |
data(GeneOverlap) go.obj <- newGeneOverlap(hESC.ChIPSeq.list$H3K4me3, hESC.ChIPSeq.list$H3K27me3, genome.size=gs.RNASeq) go.obj <- testGeneOverlap(go.obj) head(getIntersection(go.obj)) head(getUnion(go.obj)) getTested(go.obj) getContbl(go.obj) getPval(go.obj) getOddsRatio(go.obj) getJaccard(go.obj)